You should check whether root is permitted to login remotely using SSH, this is configured in the
/etc/ssh/sshd_config file. You can either use the cpanel File Manager to open the file and edit the directives, or login to SSH as a local user and then change to the
root user with the
su - command.
From the console the commands to check is;
# grep -i Root /etc/ssh/sshd_config
# the setting of "PermitRootLogin without-password".
If you need to Change
PermitRootLogin yes then you will also have to restart the sshd service.
Also, it is not clear that the users for WHM and local user accounts are using the same password database. According to the cpanel docs it looks like the
root user to login to WHM is also the system
root user - http://docs.cpanel.net/twiki/bin/view/AllDocumentation/CpanelDocs/Glossary#QqR
So it would seem that the problem use due to